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A framework for quality control in quantitative proteomics.
Tsantilas, Kristine A; Merrihew, Gennifer E; Robbins, Julia E; Johnson, Richard S; Park, Jea; Plubell, Deanna L; Canterbury, Jesse D; Huang, Eric; Riffle, Michael; Sharma, Vagisha; MacLean, Brendan X; Eckels, Josh; Wu, Christine C; Bereman, Michael S; Spencer, Sandra E; Hoofnagle, Andrew N; MacCoss, Michael J.
Afiliación
  • Tsantilas KA; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Merrihew GE; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Robbins JE; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Johnson RS; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Park J; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Plubell DL; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Canterbury JD; Thermo Fisher Scientific, 355 River Oaks Parkway, San Jose, California 95134, United States.
  • Huang E; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Riffle M; Department of Biochemistry, University of Washington, Washington 98195, United States.
  • Sharma V; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • MacLean BX; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Eckels J; LabKey, 500 Union St #1000, Seattle, Washington 98101, United States.
  • Wu CC; Department of Genome Sciences, University of Washington, Washington 98195, United States.
  • Bereman MS; Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607.
  • Spencer SE; Canada's Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada.
  • Hoofnagle AN; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States.
  • MacCoss MJ; Department of Genome Sciences, University of Washington, Washington 98195, United States.
bioRxiv ; 2024 Aug 11.
Article en En | MEDLINE | ID: mdl-38645098
ABSTRACT
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share vignettes applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis (Skyline), longitudinal QC metrics (AutoQC), and server-based data deposition (PanoramaWeb). We propose that this integrated approach to QC is a useful starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible. Data are available on Panorama Public and on ProteomeXchange under the identifier PXD051318.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Idioma: En Revista: BioRxiv Año: 2024 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos